Download Tool for Visualisation the Gene Loci of Multple Genes

Udhayakumar Mani et al /J. Pharm. Sci. & Res. Vol. 6(11), 2014, 347-350
Tool for Visualisation the Gene Loci of Multple
Genes
Udayakumar Mani, M. Krishna Nishand , G. Raghu Ram
Department of Bioinformatics,
SASTRA University, Tanjore - 613401,
Tamil Nadu, India
Abstract:
NCBI contains the chromosome location for a particular gene of our interest. When we work on genes, causing a disease, it will be
very cumbersome and time consuming to check the location of each and every gene to find out the effect of it. Not all disease causing
gene loci can be represented at a single time. We consider the array express data set. Some of the chromosome gene loci are
not been inputted in the data set. To address these problems, we have found out a visualization tool which can graphically represent
all the disease causing genes for a particular disease. This tool retrieves gene loci information from the genbank database and the
dataset is updated. The intuitive front end of the tool makes it convenient and easy for people studying that disease and gets their
gene location at a single click.
Keywords: Chromosomes, Gene Locations, Ideogram, Graphical Representation.
INTRODUCTION
Human body cells have 46 chromosomes, made up of 23
pairs. There are 44 chromosomes numbered 1-22 called
autosomes according to size from the smallest to the
largest and two sex chromosomes: X and Y. The
chromosomes consist of two very long thin strands of
DNA chains twisted into the shape of a double helix and
are located in the nucleus our body cells. The
chromosomes are long strands of genes. Since the
chromosomes come in pairs, the genes also come in pairs.
Genes are also located in very small compartments called
mitochondria that are randomly scattered in the cytoplasm
of the cell outside the nucleus. Different genes are
active in different cell types, tissues and organs,
producing the necessary specific proteins. Some genes are
‘switched off’ and others are ‘switched on’. Changes to
the genetic code can mean that a particular protein is not
produced properly, produced in the wrong amounts or not
produced at all.
Figure 1: Nomenclature of chromosome
Table 1: Nomenclature explanation
Component
7
q
31.2
Explanation
The chromosome number.
The position is on the chromosome's short arm (p
for petitin French); q indicates the long arm
(chosen as next letter in alphabet after p).
The numbers that follow the letter represent the
position on the arm: region 3, band 1, and subband 2.
NCBI gene locator:
The Map Viewer [3] provides special browsing
capabilities for a subset of organisms in Entrez
Genomes. The organism subset is shown and also on the
Map Viewer. Map Viewer allows you to view and search
an organism's complete genome, display chromosome
maps, and zoom into progressively greater levels of detail,
down to the sequence data for a region of interest. The
number and types of available maps vary by organism,
and are described in the data and search tips file for each
organism. The chromosome-specific view shows one or
more detailed maps for a single chromosome. The
results of a genome-wide search include a graphic of all
the chromosomes (to scale), with red tick marks showing
the location of markers that contained search term. The
search terms can be clone name, gene symbol, gene name,
marker name, aliases and text word
Figure 2: NCBI chromosomal representation at
location: 7q31.2
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Udhayakumar Mani et al /J. Pharm. Sci. & Res. Vol. 6(11), 2014, 347-350
NCBI [1] contains the chromosome location for a
particular gene of our interest. When we work on genes,
causing a disease, it will be very cumbersome and time
consuming to check the location of each and every gene to
find out the effect of it. Not all disease causing gene loci
can be represented at a single time. To overcome this
problem a tool has been developed which can
graphically represent all the disease causing genes for a
particular disease.
Figure 3: Dataflow diagram
Input Data:
Here we consider schizophrenia disease. The gene ids
for schizophrenia are obtained from ArrayExpress [2].
Human-affy_HG-U133_Plus_2_2007-12-04.
The
annotation file is used as input for the tool. In general, to
analyze we can use any input array express annotation file
and further process can be done.
Storage:
The data is stored in MySQL database. The interface
for storing data is done using php (hypertext preprocessor). The clone ids, genbank ids, Entrez ids, unigene
id and chromosome positions are stored in the database.
Each id is useful in retrieving the chromosome positions
of the genes.
Processing:
Using the MySQL queries, the gene ids are retrieved
from the database which does not have chromosomal
location. The respective Entrez ids are used to obtain the
missing gene loci. The retrieval is done using Perl
programming. LWP module is used. This module
retrieves the whole html web page which is obtained from
the required URL. This LWP module is not an inbuilt
package. It can be downloaded from perl.org website.
Install this LWP module and location can be obtained.
http://www.ncbi.nlm.nih.gov/gene/ followed by the Entrez
id downloads the whole html page. This page is in XML
(Extensible Markup Language) format. This XML file is
converted into text format. Using regular expression
which is a very important function of the Perl language
helps in recognizing the chromosome location. The gene
position patter is used to identify the exact gene location.
The identified gene location is updated back into the
database using the php and MySQL queries.
Representation:
The gene location is displayed as a .png (portable network
graphics) i m a g e using the graphics. The inbuilt graphics
module GD module present in php is used for the
representation. An image which exemplifies 23
chromosomes with all the gene loci is visualized
simultaneously. First all 23 chromosomes are generated
using php graphics functions. The retrieved gene loci
values are represented on their respective chromosome
region.
RESULTS AND DISCUSSION
The integrated tool can actually visualize the gene loci of
multiple genes on a single platform or on a single shot.
The aim of this project has been to help people who
study a disease. While the drawback of NCBI has been
that not all genes’ chromosome location can be identified
at the same time or to an extent visualized. This
drawback in NCBI has been overcome using the project.
We require files from ArrayExpress and the first file to
be loaded is the annotation file from ArrayExpress which
contains
the
CLONE_ID,
GENBANK_ACC,
REFSEQ_ACC,
ENTREZ_ID,
UNIGENE_ID,
GENE_SYMBOL,
GENE_TITLE
and
the
CHROMOSOME_POSITION. These data are some of
the parameters for the genes that are to be taken into
consideration for the process below. First we load into
the database which may or may not have their
chromosome positions intact.
Figure 4: Input page
The file that is loaded into the database shows the
following output is generated. Now all the contents are
stored into the database in their respective attributes and the
data needed for us is in an organized manner.
Figure 5: Tabulated output of the location of each
unknown gene on a chromosome
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Udhayakumar Mani et al /J. Pharm. Sci. & Res. Vol. 6(11), 2014, 347-350
Once the data is stored into the database, we get a
confirmation saying that all the records have been safely
stored in the database and hence we have gone for the next
step. That will be to retrieve the chromosome positions of
those genes which do not have their positions specified.
The Bioperl file will run which will retrieve all the
information from the XML file that is downloaded from
NCBI. The above program is an illustration of how we
exactly retrieve information from NCBI using an XML
format. It actually first connects with the database that is
present in the local server and takes those genes whose
chromosome positions are not specified. It then goes to
the URL of NCBI, i.e. www.ncbi.nlm.nih.gov/gene/
GENE_ID.
GENE_ID is the one the Gene id for a
particular gene in NCBI. It fetches the information and
stores in back to the database in the local server. Now we
have all information required for building up the tool. So
the pre- processes are over. Now that the file is ready, we
will compile the above Bioperl file and the output
generated will be like this:
Thus is the exact representation of the genes in the
chromosomes as we can clearly see all the genes are
located on the 23 chromosomes available with the shorter
hand that is the p hand at the top and the longer hand that is
the q hand below. Now all the genes can be significantly
represented without any glitches simultaneously and on a
single
representation
comfortably.
A
magnified
representation of the image file would be like Figure 8
Thus this is the representation of all the genes on the
chromosome for first 8 chromosome location. This is a
representation of the longer and the shorter hand and the
gene id which has been plotted on the chromosome
number. This is for all the disease causing genes and the
innovation lies in the representation of the genes on a
single platform or on a single image file.
Figure 8: Magnified image of the output
SAMPLE CODE:
Figure 6: Tabulated output of the location of each
known gene on a chromosome
The generated output actually shows the location of all
genes contained in the annotation file and hence we will
have the all the inputs ready by our side. Now we need to
plot all the diseased chromosomes on a plot which is a
graphical representation which can be in any image file
format namely, .jpg and .png formats. The representation
will be like having all the 23 chromosomes on a single
representation and hence we will have to plot all the genes
on those 23 chromosomes to be plotted in a single image
file or in a single shot representation.
Chromosome locus:
The location of a gene on a chromosome is called as locus.
It is normally represented as 8p21.3
<?php
error_reporting(0);
echo"<body bgcolor='cornsilk'><center><h1><font
color=green>CHROMOSOME
LOCATOR</h1></font";
$pname=$_FILES['f']['name'];
$ploc=$_FILES['f']['tmp_name'];
if(move_uploaded_file($ploc,"file/data.txt"))
{echo "<h2>FILE UPLODADED
SUCCESSFULLY!!!</h2><br>";}
else
{echo "Upload error";}
mysql_connect("localhost","root","");
mysql_select_db("gene1");
mysql_query("truncate data");
$k="load data local infile
'C:/wamp/www/Project/gene/file/data.txt' into table data";
mysql_query($k) or die(mysql_error());
$f=mysql_query("select CLONE_ID,ENTREZ_ID,CHROMPOs
from data limit 5");
echo "<form method=post action='/cgi-bin/loc.pl'><input
type=submit value='Click here to
find the unknown gene location'><br><br></form></a>";
echo "<center><center><table border=1><tr><td><B>Clone
ID</td><td><b>Entrez
ID</td><td><B><center>Chromosome Position</td></tr>";
while($r=mysql_fetch_array($f))
{$a1=$r[0];$a2=$r[1];$a3=$r[2];
echo "<tr><td>$a1</td><td>$a2</td><td>$a3</td></tr>";}
?>
Figure 7: Pictorial image of the output
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Udhayakumar Mani et al /J. Pharm. Sci. & Res. Vol. 6(11), 2014, 347-350
CONCLUSION
A locatable region of genomic sequence, corresponding to
a unit of inheritance, which is associated with regulatory
regions, transcribed regions, and or other functional
sequence regions
ACKNOWLEDGEMENT
We thank Department of Bioinformatics, SASTRA
University for providing us the facilities to successfully
carry forwards and complete the research project.
REFERENCES
NCBI website:
http://www.ncbi.nlm.nih.gov/. Accessed on
November 12 2011
[2]. ArrayExpress website http://www.ebi.ac.uk/arrayexpress/. Accessed
on November 13 2011)
[3]. NCBI Map Viewer:
http://www.ncbi.nlm.nih.gov/mapview/static/MapViewerHelp.html.
Accessed on November 14 2011.
[1].
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